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Sample GSM647482 Query DataSets for GSM647482
Status Public on Dec 31, 2010
Title SNB-19
Sample type RNA
 
Source name Cell line
Organism Homo sapiens
Characteristics barcode: 1_US45103081_13733329_S01_Cropped
sample tag: CNS:SNB_19
cell line: SNB-19
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the individual cell lines using Trizol (Invitrogen)
Label Hy3
Label protocol A total of 1000 ng of total RNA was used for each sample. MiRCURY™ LNA microRNA Power labeling Kit (Exiqon, Vedbaek, Denmark) was used following the manufacturers’ recommendations. Spike-ins (used as control probes) were added in equal amounts to each reaction and labeled.
 
Hybridization protocol Hybridization was performed in the hybridization station (Tecan Group Ltd., Männedorf, Switzerland), for 16 hours followed by stringency washes.
Scan protocol Subsequently, slides were dried and scanned. The analysis were performed using the relevant GenePix® Array Lists (GAL files) www.exiqon.com.
The arrays were scanned by the Agilent scanner (Agilent Technologies, Santa Clara, CA, USA), to generate Tagged Image File Format (TIFF) images. The intensities were converted to digital values using Imagene version 7.0 software. The quality control of the spots was performed by the software and adjusted manually.
Description SNB_19_CNS
Data processing The text files, generated by Imagene v.8.0, were imported into Rosetta Resolver and normalized as previously described. The data used are median of replicate spots from normalized values using the Quantile normalization method in limma package in R version 11 as descriped in Søkilde et al. (MICRORNA EXPRESSION ANALYSIS BY LNA ENHANCED MICROARRAYS)
 
Submission date Dec 30, 2010
Last update date Dec 31, 2010
Contact name Rolf Søkilde
E-mail(s) rolf.soekilde@gmail.com
Organization name Lund University, Sweden
Department Department of Oncology
Street address Scheelevägen 2
City Lund
ZIP/Postal code 221 85
Country Sweden
 
Platform ID GPL11039
Series (1)
GSE26375 MicroRNA expression profiling using microRNA microarrays on NCI-60 cell lines.

Data table header descriptions
ID_REF
VALUE normalized log2 Expression

Data table
ID_REF VALUE
3320 13.19626921
17748 12.27673058
17888 7.366884708
17834 6.365785386
17749 11.88982068
19004 12.09129644
10914 11.79967043
17750 8.749390541
13169 6.713611573
17751 8.366051293
17813 6.376111762
17752 7.955957325
17829 6.462343417
19602 6.714750748
17845 6.535763139
9938 9.223177572
19580 8.960896474
17913 6.342550799
10916 6.542859974
30773 7.649170327

Total number of rows: 1151

Table truncated, full table size 20 Kbytes.




Supplementary file Size Download File type/resource
GSM647482.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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